Dear Geraldine_VdAuwera: I also get this error message when running the HaplotypeCaller. Everything else worked fine. What do you mean by a problem in your server setup? Could you be a bit more specific? Thank you very much!

Thank you for your answer!
I've now upgraded java to the latest version, as this was suggested elsewhere for SIGSEGV errors. Now I get the following error (It occurs when executing the HaplotypeCaller) and I don't think this is a server setup problem (not that I know that much about java ..

ERROR stack trace

java.lang.NegativeArraySizeException
at org.broadinstitute.sting.utils.SWPairwiseAlignment.align(SWPairwiseAlignment.java:95)
at org.broadinstitute.sting.utils.SWPairwiseAlignment.(SWPairwiseAlignment.java:79)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.SimpleDeBruijnAssembler.addHaplotype(SimpleDeBruijnAssembler.java:335)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.SimpleDeBruijnAssembler.findBestPaths(SimpleDeBruijnAssembler.java:293)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.SimpleDeBruijnAssembler.runLocalAssembly(SimpleDeBruijnAssembler.java:69)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:394)
at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:107)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:285)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(TraverseActiveRegions.java:230)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:205)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:131)
at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:28)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:74)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)